Lecture 12 - Mutualisms and Microbiomes - BIS2C

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
BIS2C
Biodiversity & the Tree of Life
Spring 2020
Lecture 12:
Mutualisms and Microbiomes
Prof. Jonathan Eisen

Anna’s Hummingbird

Otter at Yolo Bypass

Learning Goals
• Understand examples of mutualistic symbiosis
• Understand the different between
commensalism and mutualism
• Understand details of the tubeworm - bacteria
symbiosis and why it was so surprising
• Understand examples of how the human
microbiome contributes to human health and
how it can be disturbed and restored

!11: Viruses and Gene Transfer
!12: Mutualisms and Microbiomes
!13: Endosymbiosis and Organelles
Lecture 12 Context

Lecture 12 Outline
• Background and Context
• Mutualisms
• The Human Microbiome

Background: Lab Connections
• Lab 2: Microbiome Group Presentation
• Lab 3: Termite hindgut symbionts
• Lab 2: Water fern symbiosis
• Lab 2: Legume - Rhizobium symbiosis
• Lab 3: Endosymbiosis

Review of Lecture 11

Lecture 11 Outline
• Background and Context
• Viruses
!Introduction to viruses
!Viral origins
!Viral diversity
• Gene transfer

General viral life cycle
https://www.youtube.com/watch?v=uIut0oVWCEg

Some Key Features of Viruses
! Noncellular
! Packaged into virion made up of:
! Genome (RNA or DNA)
! Protective coat (capsid)
! Sometimes additional coatings such as a lipid envelope
! Life history
! Obligately symbiotic and intracellular
! Replicate but only with assistance from host
! Causative agents of 1000s of known diseases including 100s in
humans
! Mutate and evolve
! Infectious via virions/virus particles
! No metabolism themselves
! Estimated to be > 10,000,000,000,000,000,000,000,000,000,000
(10^31) virions on earth.

Reasons
for
“No”
! Noncellular
! Life history
humans
! Mutate and evolve
! Estimated to be > 10,000,000,000,000,000,000,000,000,000,000

Reasons
for
“Yes”
! Noncellular
! Life history
humans
! Mutate and evolve
! Estimated to be > 10,000,000,000,000,000,000,000,000,000,000

Four Main Hypothesis Regarding the Origin of Viruses
Bacteria Prok Archaea Eukaryotes
Four Main Hypothesis
Regarding the Origin of
Viruses.

Diversity of viruses

Transfer of Function Via Plasmids
Exchange

Lateral gene transfer (LGT) vs Sexual Recombination
• Direction
!Sexual recombination is bidirectional with DNA from
two parental lineages mixing
!LGT is unidirectional with DNA moving from one
organism to another.
• Amount of genome
!LGT involves usually small portions of a genome
!Sexual recombination involves whole genomes.
• Relatedness
!LGT can occur across vast evolutionary distances (but
most common among close relatives).
!Sexual recombination usually within species but
sometimes more distant relatives

Classes of symbiosis
Organism
Class of symbiosis A B
Mutualism + +

Eukaryotes Need Help
• Eukaryotes as a group are somewhat limited
in their metabolic capabilities
• However, eukaryotes are remarkably adept
at “acquiring” capabilities by engaging in
mutualistic symbioses with other organisms
• In many of these the symbionts are inside
the eukaryotic cells. This may be related to
the ability of eukaryotes to undergo
phagocytosis

Mutualistic Symbioses of Bacteria w/ Eukaryotes
• Digestive
! Ruminants
! Cellulolytic insects
• Defensive
• Behavioral
! Squid light organs
• Autotrophic
! Photosynthetic (many)
! Chemosynthetic in deep sea
• Nutritional
! Aphids
! Nitrogen fixation in legumes

I Contain Multitudes Video from Tangled Bank Studios
https://youtu.be/8W_ywzhkR90

Tubeworms and Me …

Thought Question
These worms with their symbionts function as
chemolithoautotrophs. This is weird because
“normal" worms and most other animals are
A: Chemolithoheterotrophs
B: Chemoorganoautotrophs
C: Chemoorganoheterotrophs
D: Photolithoautotrophs

These worms with their symbionts function as
chemolithoautotrophs. This is weird because
“normal" worms and most other animals are
A: Chemolithoheterotrophs
B: Chemoorganoautotrophs
C: Chemoorganoheterotrophs
D: Photolithoautotrophs
Thought Question

Human Microbiome
• We are covered in a cloud of microbes
• This “microbiome” (community of microbes) likely
is involved in many important human phenotypes
• Microbiomes also are involved in health and
functioning of other organisms & ecosystems

Organism
Mutualism + +
Commensalism + 0

Organism
Mutualism + +
Commensalism + 0
Microbes in human microbiome likely benefit.
Many interactions with human microbiome likely
“commensalism” because we do not know effect on humans

Organism
Mutualism + +
Some associations in the human microbiome
appear to be mutualistic

Questions about the Human Microbiome
• Who is there?
• How do they vary?
• What are they doing?
• How do they go wrong?
• How do we fix this?
• Today we focus on three stories

Story 1: The Obese Mouse

Human Microbiome Involved in Many Functions

Human Microbiome Involved in Many Functions
• Digestion
• Vitamin Production
• Protection from parasites / pathogens
• Metabolic rate
• Immune regulation
• Odor
• Tumor development
• Behavior and mood

Story 2: Disturbing the Microbiome
Antibiotics
Diet Changes
Hygiene
C-sections
Story 2: Disturbing the Microbiome (vs expected)

• `
I Contain Multitudes Video from Tangled Bank Studios

Story 3: Restoring the Microbiome
• C-section story is an example of attempting
to restore a disturbed microbiome
• Many other examples

Restoring the Microbiome: Probiotics and Prebiotics

Restoring the Microbiome: Coprophagia

Restoring the Microbiome: Transfaunation
• http://4.bp.blogspot.com/-ojOdQeA56Fk/
UDUTQsasvRI/AAAAAAAAhtg/
aWotjwTeT4c/s1600/Untitled2.jpg

Restoring the Microbiome: Last Example …
• Clostridium difficile
• Can cause persistent GI
infections
• Antibiotics frequently do
not help
• People can have this for
decades
• Kills 30,000+ per year in
US
• Spore forming member of
Firmicutes group

Bacteria: Firmicutes
• Gram positive
• Some produce endospores
• Many of agricultural and
industrial use
• Some have no cell wall
and are extremely small
• Includes causes of:
• Anthrax
• MRSA
• Botulism
• Tetanus
Mycoplasmas
• C. diff

Restoring the Microbiome: Last Example …
• Clostridium difficile
• Can cause persistent GI
infections
• Antibiotics frequently do
not help
• People can have this for
decades
• Kills 30,000+ per year in
US
• Spore forming member of
Firmicutes group
So what can
one do?

Restoring the Microbiome: Fecal “transplants”
FECAL
TRANSPLANTS

Openbiome

DIY Fecal Transplant

Proceed With Caution …

Microbiomes
• Microbiomes are everywhere
• Major impact of health and well being of
many species
• 100s of faculty at UC Davis work on
microbiomes of various kinds

Good Luck on the Test
Lecture 12 Context

Lecture 12 - Mutualisms and Microbiomes - BIS2C

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